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Transfer Files from Basespace
# directory we are going to mount with BaseMount; create it and mount it!
basepace_dir="$HOME/BaseSpace"
mkdir -p "$basepace_dir"
basemount "${basepace_dir}/"
# ID of the project we are interested in
project_ID="NS17-03"
# run the transfer script
/ifs/data/molecpathlab/scripts/transfer_BaseSpace_to_quicksilver.sh "$project_ID" "$basepace_dir"
# unmount your BaseSpace directory when finished
basemount --unmount "${basepace_dir}/"
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NOTE: Your HPC user account may need to be a member of the
fuseuser group forbasemountto work; contact the HPC admins about this if you get permissions errors when trying to usebasemount
If the Next-Seq DNA sequencer is set to demultiplex its run data with the BaseSpace Cloud app, then the final demultiplexed fastq files need to be transferred back to the phoenix server for further analysis.
This workflow will show you how to mount a BaseSpace account on the HPC server so you can copy these files.
BaseMount Help Page:
https://help.basespace.illumina.com/articles/descriptive/introduction-to-basemount/
Before you start:
- in a web browser, log into the Basespace account holding the runs to be transferred
- if applicable, make sure the Basespace account has loaded the associated group that has your desired projects
- e.g. if your project is under your Personal account, then switch to your Personal account in BaseSpace before you start
BaseMount is already installed on the phoenix server. You just need to create and mount a directory to load the files into
# directory we are going to mount with BaseMount; create it and mount it!
basepace_dir="$HOME/BaseSpace"
mkdir -p "$basepace_dir"
basemount "${basepace_dir}/"
Now you will get a BaseMount message with a URL to open in your BaseSpace account; copy/paste the URL into the web browser
Should look like this:
#
# ,-----. ,--. ,--. ,--.
# | |) /_ ,--,--. ,---. ,---. | `.' | ,---. ,--.,--.,--,--, ,-' '-.
# | .-. \' ,-. |( .-' | .-. :| |'.'| || .-. || || || \'-. .-'
# | '--' /\ '-' |.-' `)\ --.| | | |' '-' '' '' '| || | | |
# `------' `--`--'`----' `----'`--' `--' `---' `----' `--''--' `--'
# Illumina BaseMount v0.15.15.1872 public 2016-12-16 10:47
#
# Command called:
# basemount /ifs/home/kellys04/projects/Clinical_580_gene_panel/BaseSpace/
# From:
# /ifs/home/kellys04/projects/Clinical_580_gene_panel
#
# Starting authentication.
#
# You need to authenticate by opening this URL in a browser:
# https://basespace.illumina.com/oauth/device?code=NwiY2
# ........
# It worked!
# Your identification has been saved.
#
# Mounting BaseSpace account.
# To unmount, run: basemount --unmount /ifs/home/kellys04/projects/Clinical_580_gene_panel/BaseSpace
This step might take a while, so its advised to run this from within screen on the server. Otherwise, be sure not to close the terminal while the script runs, or kill the running process.
# ID of the project we are interested in
project_ID="NS17-03"
# run the transfer script
/ifs/data/molecpathlab/scripts/transfer_BaseSpace_to_quicksilver.sh "$project_ID" "$basepace_dir"
# unmount your BaseSpace directory when finished
basemount --unmount "${basepace_dir}/"
Authentication
The first time you run BaseMount, you will be directed to a web URL and asked to enter your BaseSpace Sequence Hub user credentials. BaseMount will use these credentials to authenticate your interactions with BaseSpace Sequence Hub. By default, the credentials are cached in your home directory and they can be password-encrypted for security, just like an ssh key.
- this means that if you need to reset your login credentials on the server with BaseMount, you can just nuke the
~/.basespacedir. It will get re-created when you start the procedure over again.